Porting a transformation from Matlab to Slicer

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1

Operating system: Windows 10
Slicer version: 4.7
Expected behavior: Transformation to match registered and transformed image in Matlab
Actual behavior: Transformation is off

Hi, I am trying to double check the results of image registration (developed in Matlab) by copying the linear transformation matrix into slicer and applying it to the image. However, I do not get the same result. In matlab I use the affine3d() function to apply a homogenous transformation to an image.

I know that there is a difference between coordinate system definitions in Matlab and Slicer (IJK to RAS), but I still can’t seem to match the registration output when trying to compensate for this. What is the correct way of porting matlab affine3d() transformations to slicer?

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Slicer works in RAS coordinate system, but transform files are written as LPS, so you need a base transform between them: multiply from left and right by diag([-1,-1,1,1]).
You might also need to invert the matrix, depending on what you need: transform to or from parent.

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Thanks, I just realised shortly after posting that the transforms are in LPS, and the above base transform works correctly!

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